MBNL proteins repress ES-cell-specific alternative splicing and reprogramming (original) (raw)

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Acknowledgements

The authors thank U. Braunschweig, J. Ellis, S. Gueroussov and B. Raj for comments on the manuscript. We acknowledge D. Torti in the Donnelly Sequencing Centre for sequencing samples; L. Lee for assisting with the splicing code analysis; J. Garner (Hospital for Sick Children Embryonic Stem Cell Facility) for preparing feeder cells; A. Piekna for morphological examination of human iPSC colonies; M. Narimatsu for assisting with chimaerism analysis; and P. Mero for assisting with cell imaging. This work was supported by grants from the Canadian Institutes of Health Research (CIHR) (to B.J.B., J.L.W., A.N., J.E. and B.J.F.), the Ontario Research Fund (to J.L.W., B.J.B., A.N. and others), the Canadian Stem Cell Network (to A.N. and B.J.B.), and by a grant from the National Institutes of Health (R33MH087908) to J.E. H.H. was supported by a University of Toronto Open Fellowship. P.J.R., M.I. and N.L.B.-M. were supported by postdoctoral fellowships from the Ontario Stem Cell Initiative, Human Frontiers Science Program Organization, and the Marie Curie Actions, respectively.

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Author notes

  1. Hong Han and Manuel Irimia: These authors contributed equally to this work.

Authors and Affiliations

  1. Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada,
    Hong Han, Manuel Irimia, Mathieu Gabut, Emil N. Nachman, Dave O’Hanlon, Valentina Slobodeniuc, Nuno L. Barbosa-Morais, Jason Moffat, Brendan J. Frey & Benjamin J. Blencowe
  2. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
    Hong Han, Azadeh Golipour, Emil N. Nachman, Jason Moffat, James Ellis, Jeffrey L. Wrana & Benjamin J. Blencowe
  3. Developmental and Stem Cell Biology, The Hospital for Sick Children, 101 College Street, Toronto, Ontario M5G 1L7, Canada,
    P. Joel Ross, Tadeo Thompson & James Ellis
  4. Center for Stem Cells and Tissue Engineering, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada,
    Hoon-Ki Sung, Iacovos P. Michael & Andras Nagy
  5. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada,
    Babak Alipanahi & Brendan J. Frey
  6. Center for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada,
    Laurent David, Azadeh Golipour, Dan Trcka & Jeffrey L. Wrana
  7. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02142, Massachusetts, USA
    Eric Wang & Christopher B. Burge
  8. Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal,
    Nuno L. Barbosa-Morais
  9. Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada,
    Andras Nagy

Authors

  1. Hong Han
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  2. Manuel Irimia
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  3. P. Joel Ross
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  4. Hoon-Ki Sung
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  5. Babak Alipanahi
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  6. Laurent David
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  7. Azadeh Golipour
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  8. Mathieu Gabut
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  9. Iacovos P. Michael
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  10. Emil N. Nachman
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  11. Eric Wang
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  12. Dan Trcka
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  13. Tadeo Thompson
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  14. Dave O’Hanlon
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  15. Valentina Slobodeniuc
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  16. Nuno L. Barbosa-Morais
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  17. Christopher B. Burge
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  18. Jason Moffat
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  19. Brendan J. Frey
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  20. Andras Nagy
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  21. James Ellis
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  22. Jeffrey L. Wrana
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  23. Benjamin J. Blencowe
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Contributions

H.H. performed experiments in Figs 1–4 and Supplementary Figs 2–9 and 11–13. M.I. performed bioinformatic analyses in Figs 1–4 and Supplementary Figs 1, 3, 7, 10 and 14, with input from N.L.B.-M. L.D. and A.G. assisted with secondary MEF reprogramming experiments and clone characterization, and D.T. generated secondary MEF lines and performed chimaerism testing. P.J.R., T.T. and M.G. performed human reprogramming experiments and iPSC characterization. H-K.S. performed teratoma assays. B.A. and B.J.F. generated splicing code data. I.P.M., H.-K.S. and D.O. assisted with ES-cell overexpression and differentiation experiments. E.W. and C.B.B. generated and analysed CLIP-seq data. E.N.N. and V.S. performed RT–PCR validation experiments. B.J.B., H.H. and M.I. designed the study, with input from J.L.W., J.E., A.N. and J.M. B.J.B., H.H. and M.I. wrote the manuscript, with input from the other authors.

Corresponding author

Correspondence toBenjamin J. Blencowe.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary References, full legends for Supplementary Tables 1-5 and Supplementary Figures 1-15. (PDF 8925 kb)

Supplementary Table 1

This file contains information on RNA-Seq datasets and samples – see Supplementary Information for full legend. (XLSX 48 kb)

Supplementary Table 2

This file contains information on Human and mouse ESC-differential AS events - Supplementary Information for full legend. (XLSX 195 kb)

Supplementary Table 3

This file contains DAVID (http://david.abcc.ncifcrf.gov/) output for functional enrichment categories for human, mouse or conserved ESC-differential AS events – see Supplementary Information for full legend. (XLSX 168 kb)

Supplementary Table 4

This file contains expression levels of the human and mouse splicing factors analyzed by RNA-Seq - see Supplementary Information for full legend. (XLSX 199 kb)

Supplementary Table 5

This file contains information on mouse ESC-differential AS events plotted in Supplementary Figure 14- see Supplementary Information for full legend. (XLSX 63 kb)

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Han, H., Irimia, M., Ross, P. et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.Nature 498, 241–245 (2013). https://doi.org/10.1038/nature12270

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